Contents

1 Introduction

2 Updates

3 Note

4 Installation

4.1 Install from Github

library(devtools)
install_github('wbaopaul/rGMAP')

4.2 Install from source codes


install.packages('path to rGMAP_1.4.tar.gz', repos = NULL, type = 'source')

5 Examples

5.1 Work on an published Hi-C data

Data from Rao et al., Cell 2014, A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping

KR normalized Hi-C data for IMR90 cell line, on chr15 with resolution 10kb

library(rGMAP)
hic_rao_IMR90_chr15   
#>             n1    n2        count
#>       1:  2001  2001 1594.4993397
#>       2:  2001  2002  173.5189748
#>       3:  2002  2002 2012.2132432
#>       4:  2001  2003    7.1718521
#>       5:  2002  2003    6.0486110
#>      ---                         
#> 3553174: 10237 10250    0.8934246
#> 3553175:  9729 10251    1.0049196
#> 3553176:  9861 10251    1.9337094
#> 3553177: 10005 10251    0.8993636
#> 3553178: 10237 10251    0.8934246
res = rGMAP(hic_rao_IMR90_chr15, index_obj = NULL, resl = 10 * 1000, dom_order = 2)
names(res)
#> [1] "tads"     "hierTads" "params"

#quickly visualize some hierarchical domains
pp = plotdom(hic_rao_IMR90_chr15, index_obj = NULL, res$hierTads, chr0 = NULL, 5950, 6900, 30, 10000)
pp$p2

5.2 Compatible with HiC-Pro output matrix and index file

  • The format of the index file (10kb for example):
chr1  0 10000   1
chr1    10000   20000   2
chr1    20000   30000   3
chr1    30000   40000   4
......
  • The format of the hic_mat data:
10  127 10.372577
10  188 4.161271
10  281 36.072713
17  5822    2.418056
......

5.3 Work on an simulated example

set.seed(1)
simu_res = data_simu('poisson-dist-hier')
true_domains = simu_res$hierTads
simu_mat = simu_res$hic_mat
predicted_domains = rGMAP(simu_mat, resl = 1)$hierTads

pp = plotdom(simu_mat, NULL, predicted_domains, NULL, 1, 1000, 20, resl = 1)
pp$p2


#true_domains
#predicted_domains

6 Session Information

devtools::session_info()
#> ─ Session info ────────────────────────────────────────────────────────────
#>  setting  value                       
#>  version  R version 3.5.1 (2018-07-02)
#>  os       macOS High Sierra 10.13.6   
#>  system   x86_64, darwin15.6.0        
#>  ui       X11                         
#>  language (EN)                        
#>  collate  C                           
#>  ctype    en_US.UTF-8                 
#>  tz       Asia/Shanghai               
#>  date     2019-02-16                  
#> 
#> ─ Packages ────────────────────────────────────────────────────────────────
#>  ! package     * version     date       lib source                        
#>    assertthat    0.2.0       2017-04-11 [1] CRAN (R 3.5.0)                
#>    backports     1.1.3       2018-12-14 [1] CRAN (R 3.5.0)                
#>    BiocManager   1.30.4      2018-11-13 [1] CRAN (R 3.5.0)                
#>    BiocStyle   * 2.10.0      2018-10-30 [1] Bioconductor                  
#>    bitops        1.0-6       2013-08-17 [1] CRAN (R 3.5.0)                
#>    bookdown      0.9         2018-12-21 [1] CRAN (R 3.5.0)                
#>    callr         3.1.1       2018-12-21 [1] CRAN (R 3.5.0)                
#>    caTools       1.17.1.1    2018-07-20 [1] CRAN (R 3.5.0)                
#>    cli           1.0.1       2018-09-25 [1] CRAN (R 3.5.0)                
#>    colorspace    1.4-0       2019-01-13 [1] CRAN (R 3.5.2)                
#>    commonmark    1.7         2018-12-01 [1] CRAN (R 3.5.0)                
#>    crayon        1.3.4       2017-09-16 [1] CRAN (R 3.5.0)                
#>    data.table    1.11.8      2018-09-30 [1] CRAN (R 3.5.0)                
#>    desc          1.2.0       2018-05-01 [1] CRAN (R 3.5.0)                
#>    devtools      2.0.1       2018-10-26 [1] CRAN (R 3.5.1)                
#>    digest        0.6.18      2018-10-10 [1] CRAN (R 3.5.0)                
#>    dotCall64     1.0-0       2018-07-30 [1] CRAN (R 3.5.0)                
#>    dplyr         0.7.99.9000 2018-11-05 [1] Github (hadley/dplyr@6123e0e) 
#>    EMD           1.5.8       2018-12-05 [1] CRAN (R 3.5.0)                
#>    evaluate      0.12        2018-10-09 [1] CRAN (R 3.5.0)                
#>    fields        9.6         2018-01-29 [1] CRAN (R 3.5.0)                
#>    fs            1.2.6       2018-08-23 [1] CRAN (R 3.5.0)                
#>    ggplot2       3.1.0       2018-10-25 [1] CRAN (R 3.5.0)                
#>    glue          1.3.0       2018-07-17 [1] CRAN (R 3.5.0)                
#>    gtable        0.2.0       2016-02-26 [1] CRAN (R 3.5.0)                
#>    htmltools     0.3.6       2017-04-28 [1] CRAN (R 3.5.0)                
#>    knitr         1.21        2018-12-10 [1] CRAN (R 3.5.1)                
#>    labeling      0.3         2014-08-23 [1] CRAN (R 3.5.0)                
#>    lattice       0.20-38     2018-11-04 [1] CRAN (R 3.5.1)                
#>    lazyeval      0.2.1       2017-10-29 [1] CRAN (R 3.5.0)                
#>    locfit        1.5-9.1     2013-04-20 [1] CRAN (R 3.5.0)                
#>    magrittr      1.5         2014-11-22 [1] CRAN (R 3.5.0)                
#>    maps          3.3.0       2018-04-03 [1] CRAN (R 3.5.0)                
#>    MASS          7.3-51.1    2018-11-01 [1] CRAN (R 3.5.0)                
#>    Matrix        1.2-15      2018-11-01 [1] CRAN (R 3.5.0)                
#>    mclust        5.4.2       2018-11-17 [1] CRAN (R 3.5.0)                
#>    memoise       1.1.0       2017-04-21 [1] CRAN (R 3.5.0)                
#>    munsell       0.5.0       2018-06-12 [1] CRAN (R 3.5.0)                
#>    pillar        1.3.1       2018-12-15 [1] CRAN (R 3.5.0)                
#>    pkgbuild      1.0.2       2018-10-16 [1] CRAN (R 3.5.0)                
#>    pkgconfig     2.0.2       2018-08-16 [1] CRAN (R 3.5.0)                
#>    pkgload       1.0.2       2018-10-29 [1] CRAN (R 3.5.0)                
#>    plyr          1.8.4       2016-06-08 [1] CRAN (R 3.5.0)                
#>    prettyunits   1.0.2       2015-07-13 [1] CRAN (R 3.5.0)                
#>    processx      3.2.1       2018-12-05 [1] CRAN (R 3.5.0)                
#>    ps            1.3.0       2018-12-21 [1] CRAN (R 3.5.0)                
#>    purrr         0.2.5       2018-05-29 [1] CRAN (R 3.5.0)                
#>    R6            2.3.0       2018-10-04 [1] CRAN (R 3.5.0)                
#>    Rcpp          0.12.19.7   2018-11-05 [1] Github (RcppCore/Rcpp@b37b6f5)
#>    remotes       2.0.2       2018-10-30 [1] CRAN (R 3.5.0)                
#>  P rGMAP       * 1.4         2019-02-16 [?] local                         
#>    rlang         0.3.1       2019-01-08 [1] CRAN (R 3.5.2)                
#>    rmarkdown     1.11        2018-12-08 [1] CRAN (R 3.5.0)                
#>    roxygen2      6.1.1       2018-11-07 [1] CRAN (R 3.5.0)                
#>    rprojroot     1.3-2       2018-01-03 [1] CRAN (R 3.5.0)                
#>    rstudioapi    0.9.0       2019-01-09 [1] CRAN (R 3.5.2)                
#>    scales        1.0.0       2018-08-09 [1] CRAN (R 3.5.0)                
#>    sessioninfo   1.1.1       2018-11-05 [1] CRAN (R 3.5.0)                
#>    spam          2.2-1       2018-12-20 [1] CRAN (R 3.5.0)                
#>    stringi       1.2.4       2018-07-20 [1] CRAN (R 3.5.0)                
#>    stringr       1.3.1       2018-05-10 [1] CRAN (R 3.5.0)                
#>    tibble        2.0.1       2019-01-12 [1] CRAN (R 3.5.2)                
#>    tidyselect    0.2.5       2018-10-11 [1] CRAN (R 3.5.0)                
#>    usethis       1.4.0       2018-08-14 [1] CRAN (R 3.5.0)                
#>    withr         2.1.2       2018-03-15 [1] CRAN (R 3.5.0)                
#>    xfun          0.4         2018-10-23 [1] CRAN (R 3.5.0)                
#>    xml2          1.2.0       2018-01-24 [1] CRAN (R 3.5.0)                
#>    yaml          2.2.0       2018-07-25 [1] CRAN (R 3.5.0)                
#> 
#> [1] /Library/Frameworks/R.framework/Versions/3.5/Resources/library
#> 
#>  P ── Loaded and on-disk path mismatch.